The --outFile option works with the --module option since TypeScript 1.8, so this can be done natively. Here's the changelog. TypeScript also automatically pulls all the dependencies that don't reside in external modules, so it's enough to only compile the main app file.

If Angular 2 doesn't switch away from SystemJS, the way to bundle your app in a single file should be as simple as compiling it with options like tsc app.ts --target ES5 --module system --experimentalDecorators --moduleResolution node --emitDecoratorMetadata --outFile app.js

After that it should be possible to bootstrap the application with something like: